Hi,

I have some VCF files, I calculated MAF with PLINK, but I also want to raw allele account for the second most common allele. I normally use a custom script that count 0/1, 1/1 but I only get the number of individuals with the ALT allele. In this case, the minor allele might be the reference which makes it a bit tricker. Is PLINK (-recodeA) the best option to continue for extracting the raw count for the minor allele? It looks a bit confusing!

Also I want to filter the SNPs based on MAF, so I only want the raw count of minor allele for rare variants. Could you help me with some example of tools or commands that can do the trick? I can work in R and shell, Python if need be. Thanks

I hope it makes sense!